I would like to compare three WGS datasets to each other, without using a reference genome. I am planning on running each set of paired end fastqs through SPAdes independently and then comparing the spades.contig files to each other.

I don't know of an alignment tool that doesn't require a reference genome as an input. I essentially want each of these files to be a reference to each other. I am also hoping for some kind of output that states the % aligned, similar to bowtie2.